# Desium Spatial multi-omics analysis
Dimensionality reduction via non-negative matrix factorization and Correlation analysis

Structure of files:
* [`./env`](env/): Python environment YAML file. Based on conda/mamba.
* [`./data`](data/): All Spatial multi-omics integrated data for DESI-MSI and VST.
* [`./README.md`]: Instruction on python environment and installation
* [`./DESIUM_Correlation_NMF_analysis.ipynb`] : Analysis example on sample LC_091

To reproduce the results in the paper on Desium Spatial multi-omics
* Read through this README.md file
* Run the example jupyter notebook provided
* Expected output and runtime is shown in the same notebook


## System requirements:
* An environment YAML file [`./env/environment.yml`] is provided to define and share a Python environment. It includes a structured list of packages, packages version, dependencies, and configuration settings necessary to recreate or replicate the environment on another system.
 

## Installation guide
* Steps to install the Python environment from 'environment.yaml' file

This environment can be setup locally by running:
```
conda env create -f environment.yml
conda activate <environment_name>
```
* Run the notebook example
```
jupyter notebook DESIUM_Correlation_NMF_analysis.ipynb
```






